ENST00000429829.6:n.10240C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000429829.6(XIST):n.10240C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 551,834 control chromosomes in the GnomAD database, including 111 homozygotes. There are 3,575 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
ENST00000429829.6 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XIST | ENST00000429829.6 | n.10240C>T | non_coding_transcript_exon_variant | Exon 1 of 6 | 1 | |||||
XIST | ENST00000648607.1 | n.1725C>T | non_coding_transcript_exon_variant | Exon 1 of 6 | ||||||
XIST | ENST00000648991.1 | n.1600C>T | non_coding_transcript_exon_variant | Exon 1 of 5 |
Frequencies
GnomAD3 genomes AF: 0.0164 AC: 1831AN: 111391Hom.: 20 Cov.: 23 AF XY: 0.0164 AC XY: 551AN XY: 33595
GnomAD3 exomes AF: 0.0158 AC: 2427AN: 153598Hom.: 28 AF XY: 0.0149 AC XY: 775AN XY: 51860
GnomAD4 exome AF: 0.0196 AC: 8640AN: 440396Hom.: 91 Cov.: 0 AF XY: 0.0185 AC XY: 3023AN XY: 163290
GnomAD4 genome AF: 0.0164 AC: 1832AN: 111438Hom.: 20 Cov.: 23 AF XY: 0.0164 AC XY: 552AN XY: 33652
ClinVar
Submissions by phenotype
XIST-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at